tool_test_output.json

{"tests": [{"data": {"status": "success", "inputs": {"inputzip": {"src": "hda", "id": "2891970512fa2d5a"}, "name_of_study": "test"}, "job": {"inputs": {"inputzip": {"src": "hda", "id": "2891970512fa2d5a", "uuid": "36f05a59-2bf5-4219-976e-c65292ec09a2"}}, "update_time": "2016-10-06T15:35:15.353432", "tool_id": "mzml2isa", "outputs": {"i_file": {"src": "hda", "id": "8155e4b4bf1581ff", "uuid": "91a11871-27f7-4b81-b21c-aae29c769b31"}, "html_file": {"src": "hda", "id": "5729865256bc2525", "uuid": "5a6c71cd-bfdf-4e72-bfce-870d31e80d27"}, "__new_primary_file_a_test_metabolite_profiling_mass_spectrometry|a_test_metabolite_profiling_mass_spectrometry__": {"src": "hda", "id": "fa6d20d0fb68383f", "uuid": "43ead1d8-8b5a-40df-84f2-50089fa48b96"}, "__new_primary_file_s_test|s_test__": {"src": "hda", "id": "7b55dbb89df8f4e5", "uuid": "9dc40dc5-7bff-4440-ad48-efb86f601b1d"}, "ISA_zip": {"src": "hda", "id": "54f2a3a23292eb07", "uuid": "8b5122ec-c63d-4c44-bb4a-fe50a0d70c60"}}, "stdout": "  adding: i_Investigation.txt (deflated 73%)\n  adding: a_test_metabolite_profiling_mass_spectrometry.txt (deflated 91%)\n  adding: s_test.txt (deflated 76%)\n", "command_line": "python /home/tnl495/mzml2isa-galaxy/galaxy/mzml2isa/wrapper.py -inputzip \"/tmp/tmpEw83A2/files/000/dataset_1.dat\" -jsontxt \"None\" -html_file \"/tmp/tmpEw83A2/files/000/dataset_2.dat\" -out_dir . -study_title \"test\" --s_submission_date \"\" --s_release_date \"\" --s_description \"\" --s_pubmed \"\" --s_pub_doi \"\" --s_pub_status \"\" --s_pub_title \"\" --s_pub_author \"\" --s_first_name \"\" --s_mid_initials \"\" --s_last_name \"\" --s_telephone \"\" --s_fax \"\" --s_affiliation \"\" --s_role \"\" --s_mail \"\" --s_address \"\" --i_submission_date \"\" --i_release_date \"\" --i_description \"\" --i_pubmed \"\" --i_pub_doi \"\" --i_pub_title \"\" --i_pub_status \"\" --i_pub_author \"\" --i_first_name \"\" --i_mid_initials \"\" --i_last_name \"\" --i_telephone \"\" --i_fax \"\" --i_affiliation \"\" --i_role \"\" --i_mail \"\" --i_address \"\" --organism_text \"\" --organism_ref \"\" --organism_iri \"\" --organism_variant_text \"\" --organism_variant_ref \"\" --organism_variant_iri \"\" --organism_part_text \"\" --organism_part_ref \"\" --organism_part_iri \"\";  ln -s ./\"test\" study_dir;  cd study_dir; zip isa.zip i_* a_* s_* && mv isa.zip \"/tmp/tmpEw83A2/files/000/dataset_3.dat\";", "exit_code": 0, "state": "ok", "create_time": "2016-10-06T15:35:11.727094", "params": {"s_contacts": "{\"s_contacts_select\": \"hide\", \"__current_case__\": 0}", "name_of_study": "\"test\"", "i_contacts": "{\"__current_case__\": 0, \"i_contacts_select\": \"hide\"}", "dbkey": "\"hg17\"", "invest_meta": "{\"__current_case__\": 0, \"invest_select\": \"hide\"}", "study_meta": "{\"__current_case__\": 0, \"study_select\": \"hide\"}", "chromInfo": "\"/tmp/tmpEw83A2/galaxy-master/tool-data/shared/ucsc/chrom/hg17.len\"", "jsontxt": "null", "exp_meta": "{\"exp_select\": \"hide\", \"__current_case__\": 0}"}, "stderr": "Parsing test    :    0/   6 |                                  | ETA:  --:--:--\rParsing test    :    1/   6 |#####                              | ETA:  0:00:00\rParsing test    :    2/   6 |###########                        | ETA:  0:00:00\rParsing test    :    3/   6 |#################                  | ETA:  0:00:00\rParsing test    :    4/   6 |#######################            | ETA:  0:00:00\rParsing test    :    5/   6 |#############################      | ETA:  0:00:00\rParsing test    :    6/   6 |###################################| Time: 0:00:00\r\n", "job_metrics": [], "model_class": "Job", "external_id": "3745", "id": "5729865256bc2525", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mzml2isa.test_tool_000000", "has_data": true}], "version": "0.1", "exit_code": 0, "summary": {"num_skips": 0, "num_errors": 0, "num_failures": 0, "num_tests": 1}}